Multi-tissue transcriptional changes and core circadian clock disruption following intensive care

Abstract

Objective: Both critical illness and current care have been hypothesized to upset daily rhythms and impair molecular circadian function. However, the influence of critical illness on clock function in different tissues and on circadian output genes are unknown. Here we evaluate the effect of critical care and illness on transcription, focusing on the functional organization of the core circadian oscillator.Methods: We downloaded RNAseq count data from the Genotype-Tissue Expression (GTEx) project. Treating mechanical ventilation as a marker for intensive care, we stratified samples into acute death (AD) and intensive care (IC) groups based on the documented Hardy Death Scale. We restricted our analysis to the 25 tissues with >50 samples in each group. Using the edgeR package and controlling for collection center, gender, and age, we identified transcripts differentially expressed between the AD and IC groups. Overrepresentation and enrichment methods were used to identify gene sets modulated by intensive care across tissues. For each tissue, we then calculated the delta clock correlation distance (ΔCCD), a comparative measure of the functional organization of the core circadian oscillator, in the both the AD and IC groups. The statistical significance of the ΔCCD was assessed by permutation, modifying a pre-existing R package to control for confounding variables.Results: Intensive care, as marked by ventilation, significantly modulated the expression of thousands of genes. Transcripts that were modulated in ≥75% of tissues were enriched for genes involved in mitochondrial energetics, cellular stress, metabolism, and notably circadian regulation. Transcripts that were more markedly affected, in ≥10 tissues, were enriched for inflammation, complement and immune pathways. Oscillator organization, as assessed by ΔCCD, was significantly reduced in the intensive care group in 11/25 tissues.Conclusion: Our findings support the hypothesis that patients in intensive care have impaired molecular circadian rhythms. Tissues involved in metabolism and energetics demonstrated the most marked changes in oscillator organization. In adipose tissue, there was a significant overlap between transcripts previously established to be modulated by sleep deprivation and fasting with those modulated by critical care. This work suggests that intensive care protocols that restore sleep/wake and nutritional rhythms may be of benefit.

Tumor circadian clock strength influences metastatic potential and predicts patient prognosis in luminal A breast cancer

“…To examine core clock organization in these breast tumors, we performed Spearman’s correlation coefficient analysis ( 27 , 31 – 33 ). We limited our analysis to paired breast tumors and non-cancerous samples with a sequencing depth > 20 million reads.…”

“…Our analysis of locally collected samples combined data from biologically distinct breast tumor types. We applied clock gene correlation analysis ( 27 , 31 – 33 ) to TCGA breast tumor data to evaluate core clock organization in cancer subtypes. The expression of the PAM50 panel genes was used to define cancer subtypes ( 42 , 43 ).…”

“…2 A ). Using a permutation test ( 32 , 33 ), we directly compared the Zstat scores of these three tumor subtypes. The correlation patterns in luminal A tumors were significantly stronger than those seen in luminal B tumors ( P = <0.01), while the Zstat scores of the luminal B and basal groups were not significantly different.…”

Sleep and Circadian Health of Critical Survivors: A 12-Month Follow-Up Study*

“…A second observation relies on a possible impact of the ICU and its setting at the molecular level, which could lead to a somewhat longer and/or irreversible condition. Previous studies demonstrate that 1 week at the ICU is sufficient to promote an overall impairment of molecular circadian rhythms, including the loss of circadian rhythmicity of several clock genes ( 39 , 40 ). Nevertheless, information on whether such alterations persist over time when the triggering factors are no longer present remains to be demonstrated.…”

Subtype-specific circadian clock dysregulation modulates breast cancer biology, invasiveness, and prognosis

“…To examine core clock organization in these breast tumors, we performed Spearman's correlation coefficient analysis 38,[41][42][43] using RNAseq data from time-stamped paired breast tumors and non-cancerous samples with a sequencing depth of >20 million reads. As expected, the non-cancerous breast tissues demonstrate core-clock correlation patterns mirroring those seen in mice 16 .…”